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- EMDB-0514: Structural insights into unique features of the human mitochondri... -
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Open data
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Basic information
Entry | Database: EMDB / ID: EMD-0514 | |||||||||
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Title | Structural insights into unique features of the human mitochondrial ribosome recycling | |||||||||
![]() | Cryo-EM structure of mammalian mitochondrial 55S ribosome with mtRRF-Class1 | |||||||||
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Function / homology | ![]() mitochondrial ribosome binding / rRNA import into mitochondrion / mitochondrial translational elongation / mitochondrial translational termination / mitochondrial ribosome assembly / microprocessor complex / translation release factor activity, codon nonspecific / Mitochondrial translation elongation / Mitochondrial translation termination / positive regulation of mitochondrial translation ...mitochondrial ribosome binding / rRNA import into mitochondrion / mitochondrial translational elongation / mitochondrial translational termination / mitochondrial ribosome assembly / microprocessor complex / translation release factor activity, codon nonspecific / Mitochondrial translation elongation / Mitochondrial translation termination / positive regulation of mitochondrial translation / Mitochondrial translation initiation / negative regulation of mitotic nuclear division / mitochondrial large ribosomal subunit / Hydrolases; Acting on ester bonds; Endoribonucleases producing 5'-phosphomonoesters / ribosome disassembly / peptidyl-tRNA hydrolase / mitochondrial small ribosomal subunit / aminoacyl-tRNA hydrolase activity / mitochondrial ribosome / mitochondrial translation / ribosomal large subunit binding / positive regulation of proteolysis / ribosomal small subunit binding / anatomical structure morphogenesis / RNA processing / Mitochondrial protein degradation / rescue of stalled ribosome / cellular response to leukemia inhibitory factor / apoptotic signaling pathway / fibrillar center / double-stranded RNA binding / cell junction / regulation of translation / ribosomal small subunit assembly / small ribosomal subunit / small ribosomal subunit rRNA binding / 5S rRNA binding / large ribosomal subunit rRNA binding / nuclear membrane / cytosolic small ribosomal subunit / endonuclease activity / cell population proliferation / mitochondrial inner membrane / tRNA binding / nuclear body / rRNA binding / negative regulation of translation / ribosome / structural constituent of ribosome / mitochondrial matrix / ribonucleoprotein complex / translation / protein domain specific binding / intracellular membrane-bounded organelle / nucleotide binding / mRNA binding / synapse / apoptotic process / nucleolus / GTP binding / mitochondrion / RNA binding / extracellular space / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | single particle reconstruction / cryo EM / Resolution: 3.9 Å | |||||||||
![]() | Sharma MR / Koripella RK / Agrawal RK | |||||||||
Funding support | ![]()
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![]() | ![]() Title: Structural insights into unique features of the human mitochondrial ribosome recycling. Authors: Ravi K Koripella / Manjuli R Sharma / Paul Risteff / Pooja Keshavan / Rajendra K Agrawal / ![]() Abstract: Mammalian mitochondrial ribosomes (mitoribosomes) are responsible for synthesizing proteins that are essential for oxidative phosphorylation (ATP generation). Despite their common ancestry with ...Mammalian mitochondrial ribosomes (mitoribosomes) are responsible for synthesizing proteins that are essential for oxidative phosphorylation (ATP generation). Despite their common ancestry with bacteria, the composition and structure of the human mitoribosome and its translational factors are significantly different from those of their bacterial counterparts. The mammalian mitoribosome recycling factor (RRF) carries a mito-specific N terminus extension (NTE), which is necessary for the function of RRF Here we present a 3.9-Å resolution cryo-electron microscopic (cryo-EM) structure of the human 55S mitoribosome-RRF complex, which reveals α-helix and loop structures for the NTE that makes multiple mito-specific interactions with functionally critical regions of the mitoribosome. These include ribosomal RNA segments that constitute the peptidyl transferase center (PTC) and those that connect PTC with the GTPase-associated center and with mitoribosomal proteins L16 and L27. Our structure reveals the presence of a tRNA in the pe/E position and a rotation of the small mitoribosomal subunit on RRF binding. In addition, we observe an interaction between the pe/E tRNA and a mito-specific protein, mL64. These findings help understand the unique features of mitoribosome recycling. | |||||||||
History |
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Structure visualization
Movie |
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Structure viewer | EM map: ![]() ![]() ![]() |
Supplemental images |
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Downloads & links
-EMDB archive
Map data | ![]() | 197.1 MB | ![]() | |
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Header (meta data) | ![]() ![]() | 92.7 KB 92.7 KB | Display Display | ![]() |
Images | ![]() | 178.7 KB | ||
Archive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6nu2MC ![]() 0515C ![]() 6nu3C M: atomic model generated by this map C: citing same article ( |
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Similar structure data |
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Links
EMDB pages | ![]() ![]() |
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Related items in Molecule of the Month |
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Map
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Annotation | Cryo-EM structure of mammalian mitochondrial 55S ribosome with mtRRF-Class1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Voxel size | X=Y=Z: 1.09 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Density |
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Symmetry | Space group: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Details | EMDB XML:
CCP4 map header:
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-Supplemental data
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Sample components
+Entire : Structural insights into unique features of the human mitochondri...
+Supramolecule #1: Structural insights into unique features of the human mitochondri...
+Macromolecule #1: 16S rRNA
+Macromolecule #2: mt-tRNAVal
+Macromolecule #54: E-site tRNA
+Macromolecule #56: 12S rRNA
+Macromolecule #3: 39S ribosomal protein L2, mitochondrial
+Macromolecule #4: 39S ribosomal protein L3, mitochondrial
+Macromolecule #5: 39S ribosomal protein L4, mitochondrial
+Macromolecule #6: 39S ribosomal protein L9, mitochondrial
+Macromolecule #7: 39S ribosomal protein L10, mitochondrial
+Macromolecule #8: 39S ribosomal protein L11, mitochondrial
+Macromolecule #9: 39S ribosomal protein L13, mitochondrial
+Macromolecule #10: 39S ribosomal protein L14, mitochondrial
+Macromolecule #11: 39S ribosomal protein L15, mitochondrial
+Macromolecule #12: 39S ribosomal protein L16, mitochondrial
+Macromolecule #13: 39S ribosomal protein L17, mitochondrial
+Macromolecule #14: 39S ribosomal protein L18, mitochondrial
+Macromolecule #15: 39S ribosomal protein L19, mitochondrial
+Macromolecule #16: 39S ribosomal protein L20, mitochondrial
+Macromolecule #17: 39S ribosomal protein L21, mitochondrial
+Macromolecule #18: 39S ribosomal protein L22, mitochondrial
+Macromolecule #19: 39S ribosomal protein L23, mitochondrial
+Macromolecule #20: 39S ribosomal protein L24, mitochondrial
+Macromolecule #21: 39S ribosomal protein L27, mitochondrial
+Macromolecule #22: 39S ribosomal protein L28, mitochondrial
+Macromolecule #23: 39S ribosomal protein L47, mitochondrial
+Macromolecule #24: 39S ribosomal protein L30, mitochondrial
+Macromolecule #25: 39S ribosomal protein L32, mitochondrial
+Macromolecule #26: 39S ribosomal protein L33, mitochondrial
+Macromolecule #27: 39S ribosomal protein L34, mitochondrial
+Macromolecule #28: 39S ribosomal protein L35, mitochondrial
+Macromolecule #29: 39S ribosomal protein L36, mitochondrial
+Macromolecule #30: 39S ribosomal protein L37, mitochondrial
+Macromolecule #31: 39S ribosomal protein L38, mitochondrial
+Macromolecule #32: 39S ribosomal protein L39, mitochondrial
+Macromolecule #33: 39S ribosomal protein L40, mitochondrial
+Macromolecule #34: 39S ribosomal protein L41, mitochondrial
+Macromolecule #35: 39S ribosomal protein L42, mitochondrial
+Macromolecule #36: 39S ribosomal protein L43, mitochondrial
+Macromolecule #37: 39S ribosomal protein L44, mitochondrial
+Macromolecule #38: 39S ribosomal protein L45, mitochondrial
+Macromolecule #39: 39S ribosomal protein L46, mitochondrial
+Macromolecule #40: 39S ribosomal protein L48, mitochondrial
+Macromolecule #41: 39S ribosomal protein L49, mitochondrial
+Macromolecule #42: 39S ribosomal protein L50, mitochondrial
+Macromolecule #43: 39S ribosomal protein L51, mitochondrial
+Macromolecule #44: 39S ribosomal protein L52, mitochondrial
+Macromolecule #45: 39S ribosomal protein L53, mitochondrial
+Macromolecule #46: 39S ribosomal protein L54, mitochondrial
+Macromolecule #47: 39S ribosomal protein L55, mitochondrial
+Macromolecule #48: Ribosomal protein 63, mitochondrial
+Macromolecule #49: Peptidyl-tRNA hydrolase ICT1, mitochondrial
+Macromolecule #50: Growth arrest and DNA damage-inducible proteins-interacting protein 1
+Macromolecule #51: 39S ribosomal protein S18a, mitochondrial
+Macromolecule #52: 39S ribosomal protein S30, mitochondrial
+Macromolecule #53: Unknown protein/protein extension
+Macromolecule #55: Ribosome-recycling factor, mitochondrial
+Macromolecule #57: 28S ribosomal protein S2, mitochondrial
+Macromolecule #58: 28S ribosomal protein S24, mitochondrial
+Macromolecule #59: 28S ribosomal protein S5, mitochondrial
+Macromolecule #60: 28S ribosomal protein S6, mitochondrial
+Macromolecule #61: 28S ribosomal protein S7, mitochondrial
+Macromolecule #62: 28S ribosomal protein S9, mitochondrial
+Macromolecule #63: 28S ribosomal protein S10, mitochondrial
+Macromolecule #64: 28S ribosomal protein S11, mitochondrial
+Macromolecule #65: 28S ribosomal protein S12, mitochondrial
+Macromolecule #66: 28S ribosomal protein S14, mitochondrial
+Macromolecule #67: 28S ribosomal protein S15, mitochondrial
+Macromolecule #68: 28S ribosomal protein S16, mitochondrial
+Macromolecule #69: 28S ribosomal protein S17, mitochondrial
+Macromolecule #70: 28S ribosomal protein S18b, mitochondrial
+Macromolecule #71: 28S ribosomal protein S18c, mitochondrial
+Macromolecule #72: 28S ribosomal protein S21, mitochondrial
+Macromolecule #73: 28S ribosomal protein S22, mitochondrial
+Macromolecule #74: 28S ribosomal protein S23, mitochondrial
+Macromolecule #75: 28S ribosomal protein S25, mitochondrial
+Macromolecule #76: 28S ribosomal protein S26, mitochondrial
+Macromolecule #77: 28S ribosomal protein S27, mitochondrial
+Macromolecule #78: 28S ribosomal protein S28, mitochondrial
+Macromolecule #79: 28S ribosomal protein S29, mitochondrial
+Macromolecule #80: 28S ribosomal protein S31, mitochondrial
+Macromolecule #81: 28S ribosomal protein S33, mitochondrial
+Macromolecule #82: 28S ribosomal protein S34, mitochondrial
+Macromolecule #83: 28S ribosomal protein S35, mitochondrial
+Macromolecule #84: Coiled-coil-helix-coiled-coil-helix domain-containing protein 1
+Macromolecule #85: Aurora kinase A-interacting protein
+Macromolecule #86: Pentatricopeptide repeat domain-containing protein 3, mitochondrial
+Macromolecule #87: MAGNESIUM ION
+Macromolecule #88: ZINC ION
-Experimental details
-Structure determination
Method | cryo EM |
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![]() | single particle reconstruction |
Aggregation state | particle |
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Sample preparation
Buffer | pH: 7.6 |
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Grid | Details: unspecified |
Vitrification | Cryogen name: ETHANE |
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Electron microscopy
Microscope | FEI TITAN KRIOS |
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Image recording | Film or detector model: GATAN K2 SUMMIT (4k x 4k) / Average electron dose: 70.0 e/Å2 |
Electron beam | Acceleration voltage: 300 kV / Electron source: OTHER |
Electron optics | Illumination mode: OTHER / Imaging mode: OTHER |
Experimental equipment | ![]() Model: Titan Krios / Image courtesy: FEI Company |